3:48 shows the location of it on the other side of the heater box. If you're looking for where it is when in the Jeep, it's somewhat hidden below the battery.
A few months ago I took this picture of some wear marks I could actually feel on my AC accumulator because the super fat wiring harness had been rubbing on it for maybe 15 yrs? Anyway, the battery is out and you can see part of the curved thing that Bleepin Jeep guy calls the down tube. It's at least a few inches below my two fingers that are blocking some view, if they were out of the way we'd probably see the whole thing.
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I kinda doubt that rain water is entering the Jeep through that area, mainly because I don't think much, if any, rain water would get there to begin with.
Was the drain plugged up? If it was, the water that wasn't draining out needed to go somewhere. Of course even if it is draining that doesn't mean something else isn't causing your water issue.
I'm not sure what you actually mean with "just flood that intake with water" but if you pour water into the heater box it should leak right out through the down tube thing. Spraying water around the cowl/air intake area with someone else's head under the dashboard should help them find out where the leak is. Just start slow, if you spray too much water everywhere at the beginning and it immediately leaks you'll only have narrowed the leak's location down to just about anywhere.